The American Academy of Microbiology convenes colloquia to address emerging issues in microbiology. The primary objective of the proposed colloquium is to provide a forum to address science opportunities and research challenges recently made evident. How will we take microbial genome sequence information back to the environment? The environment is the context in which genomes evolved, function, and continue to evolve. It is the only context in which they can be fully understood. We suggest that we explicitly evaluate possible new roles of microbial systematics. What role will microbial systematics play in providing order to the immense amount of genomic information now being generated? How is genomic information "packaged" in the environment? What is the relationship between genome sequence and phenotype? What is comparative genomics telling us about the basic mechanisms of evolution and adaptive radiation? This colloquium will bring together a diverse group of scientists working on issues related to systematics, ecology, and genomics. The colloquium format, so successful in the past, is a meeting designed to encourage thoughful discussion on a list of questions developed by the colloquium's steering committee. Participants engage in these discussions throughout the weekend in interdisciplinary working groups, analyzing the issues and developing practical recommendations for the future. The colloquium report will be global and multidisciplinary in its perspective. It will be analytical and comprehensive, yet offer practical recommendations. In short, the colloquium should help crystallize a new conceptual understanding of why the microbe is as it is, from integrating genomic, evolutionary, ecological and physiological information, and to identify the knowledge gaps which if answered will allow better predictions and management of a major portion of our biosphere. Following the colloquium, an outreach plan will be developed for dissemination of the report.